Multiple sequence alignment - TraesCS4D01G155000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G155000 chr4D 100.000 2531 0 0 1 2531 206975315 206972785 0 4674
1 TraesCS4D01G155000 chr1B 95.392 2539 107 9 1 2531 633711266 633713802 0 4032
2 TraesCS4D01G155000 chr5D 95.353 2539 109 9 1 2531 6258806 6256269 0 4026
3 TraesCS4D01G155000 chr5D 95.274 2539 112 7 1 2531 503307969 503310507 0 4017
4 TraesCS4D01G155000 chr1D 95.191 2537 102 10 1 2531 254451112 254453634 0 3991
5 TraesCS4D01G155000 chr1D 94.720 2538 118 13 1 2531 51837657 51835129 0 3930
6 TraesCS4D01G155000 chr1A 95.156 2539 94 8 1 2531 554476557 554479074 0 3980
7 TraesCS4D01G155000 chr6B 94.482 2537 110 14 1 2531 18743962 18741450 0 3882
8 TraesCS4D01G155000 chr4A 94.289 2539 132 13 1 2531 309452099 309449566 0 3873
9 TraesCS4D01G155000 chr5A 94.537 2453 115 12 85 2531 85547137 85549576 0 3770


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G155000 chr4D 206972785 206975315 2530 True 4674 4674 100.000 1 2531 1 chr4D.!!$R1 2530
1 TraesCS4D01G155000 chr1B 633711266 633713802 2536 False 4032 4032 95.392 1 2531 1 chr1B.!!$F1 2530
2 TraesCS4D01G155000 chr5D 6256269 6258806 2537 True 4026 4026 95.353 1 2531 1 chr5D.!!$R1 2530
3 TraesCS4D01G155000 chr5D 503307969 503310507 2538 False 4017 4017 95.274 1 2531 1 chr5D.!!$F1 2530
4 TraesCS4D01G155000 chr1D 254451112 254453634 2522 False 3991 3991 95.191 1 2531 1 chr1D.!!$F1 2530
5 TraesCS4D01G155000 chr1D 51835129 51837657 2528 True 3930 3930 94.720 1 2531 1 chr1D.!!$R1 2530
6 TraesCS4D01G155000 chr1A 554476557 554479074 2517 False 3980 3980 95.156 1 2531 1 chr1A.!!$F1 2530
7 TraesCS4D01G155000 chr6B 18741450 18743962 2512 True 3882 3882 94.482 1 2531 1 chr6B.!!$R1 2530
8 TraesCS4D01G155000 chr4A 309449566 309452099 2533 True 3873 3873 94.289 1 2531 1 chr4A.!!$R1 2530
9 TraesCS4D01G155000 chr5A 85547137 85549576 2439 False 3770 3770 94.537 85 2531 1 chr5A.!!$F1 2446

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
563 588 0.682855 ACGAGAGCCCAGAGGAAGAG 60.683 60.0 0.0 0.0 33.47 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2196 1.758862 CCAATCAAGAATCCCCAAGGC 59.241 52.381 0.0 0.0 0.0 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.582689 ATCCTGTTTTGGGATTTCGATTC 57.417 39.130 0.00 0.00 40.31 2.52
54 55 3.719479 TCGATTCAAATCCCCCTTATGGA 59.281 43.478 0.00 0.00 36.05 3.41
63 64 5.742562 ATCCCCCTTATGGATGTTTTACA 57.257 39.130 0.00 0.00 41.10 2.41
99 100 6.567687 TTTTGCTTATTTTGACGATCTCCA 57.432 33.333 0.00 0.00 0.00 3.86
105 106 7.335673 TGCTTATTTTGACGATCTCCAATACAA 59.664 33.333 0.00 0.00 0.00 2.41
175 178 7.120138 CCCTAGAAGAAGAATATAGGACTCGAC 59.880 44.444 0.00 0.00 35.97 4.20
186 210 1.424635 GACTCGACCGGAAGACTCG 59.575 63.158 9.46 6.79 33.90 4.18
437 461 2.698797 GGACCCAAGAGGACGAATATGA 59.301 50.000 0.00 0.00 39.89 2.15
443 467 4.811557 CCAAGAGGACGAATATGAAACTCC 59.188 45.833 0.00 0.00 36.89 3.85
453 477 6.098982 ACGAATATGAAACTCCAGAGGAAGAT 59.901 38.462 0.00 0.00 0.00 2.40
473 497 5.862845 AGATTCAGAAGACGAATATGGCAT 58.137 37.500 4.88 4.88 33.26 4.40
478 502 0.693049 AGACGAATATGGCATCCCCC 59.307 55.000 1.65 0.00 0.00 5.40
563 588 0.682855 ACGAGAGCCCAGAGGAAGAG 60.683 60.000 0.00 0.00 33.47 2.85
597 622 5.813513 AAAAGAGGGTTTGATTGAGCATT 57.186 34.783 0.00 0.00 0.00 3.56
609 634 6.349243 TGATTGAGCATTGAGGAACAAAAT 57.651 33.333 0.00 0.00 42.03 1.82
647 673 5.074584 ACCAAAGAGAAGTAGATCGGTTC 57.925 43.478 0.00 0.00 0.00 3.62
686 712 4.264460 ACTTCATATCTTGCCGAGATCC 57.736 45.455 0.00 0.00 44.04 3.36
694 720 1.410850 TTGCCGAGATCCTCATCCCC 61.411 60.000 0.00 0.00 0.00 4.81
879 910 1.398390 GCTGTTTGATACCGCCAGAAG 59.602 52.381 0.00 0.00 31.47 2.85
986 1021 2.188062 TTTGTTTCCGTTCGCCCTAT 57.812 45.000 0.00 0.00 0.00 2.57
1073 1108 9.643693 GCAAGAAGAAAATAATCTCCAAATTCA 57.356 29.630 0.00 0.00 0.00 2.57
1193 1228 6.212589 TGGGAACAAGAAGAAAAAGAAAAGGT 59.787 34.615 0.00 0.00 37.44 3.50
1217 1252 3.421844 GTGCTTCCCTTGTTGAGGTAAT 58.578 45.455 0.00 0.00 44.71 1.89
1252 1287 9.706691 ATCTTATTCGCGATTTCCTAAGAATTA 57.293 29.630 10.88 0.00 31.24 1.40
1258 1293 8.123445 TCGCGATTTCCTAAGAATTAAGTTAC 57.877 34.615 3.71 0.00 0.00 2.50
1261 1296 8.549548 GCGATTTCCTAAGAATTAAGTTACTCC 58.450 37.037 0.00 0.00 0.00 3.85
1356 1391 6.963796 AGATCGCACCAATATCAATTCTTTC 58.036 36.000 0.00 0.00 0.00 2.62
1471 1506 1.621317 TGTCGGCATCCAACTGTTCTA 59.379 47.619 0.00 0.00 0.00 2.10
1528 1563 6.966534 ATGCGATAAAAGAATGGAATCCTT 57.033 33.333 0.00 0.00 0.00 3.36
1774 1812 7.122650 GGATCCATTCCTTTTGAATTGTCACTA 59.877 37.037 6.95 0.00 41.85 2.74
1818 1856 7.231317 GGGAAGAGATATTGGCAATAATTCACA 59.769 37.037 22.65 1.45 0.00 3.58
2050 2090 5.290493 AGTGACATAACACAAGGTCTTCA 57.710 39.130 0.00 0.00 42.45 3.02
2074 2114 8.093927 TCAAAAAGTGGAACAAATCTTTGAAGT 58.906 29.630 9.53 0.00 44.16 3.01
2098 2138 7.616935 AGTGTGTTCAATTGATTCATTATCCCT 59.383 33.333 9.40 0.00 31.87 4.20
2181 2221 3.122480 TGGGGATTCTTGATTGGAGCTA 58.878 45.455 0.00 0.00 0.00 3.32
2251 2291 2.039418 GGTTTATTGATCCCAAGGGGC 58.961 52.381 5.08 0.00 43.94 5.80
2318 2358 1.950909 TCAAAAGTGCGGGTTTTCGAT 59.049 42.857 0.00 0.00 0.00 3.59
2349 2389 2.040545 TCTAATGTTTTTCCGCCTGGGA 59.959 45.455 0.00 0.00 45.40 4.37
2416 2456 7.494922 TGGATGAATCGATCTATTATTGGGA 57.505 36.000 0.00 0.00 0.00 4.37
2494 2534 4.158394 AGCAAGTTTTCAAGAAACTGCTCA 59.842 37.500 15.04 0.00 38.74 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.955961 AAAACATCCATAAGGGGGATTTG 57.044 39.130 0.00 0.00 42.47 2.32
105 106 8.713971 ACAATTCCTGAACCCTTTTATCTTTTT 58.286 29.630 0.00 0.00 0.00 1.94
186 210 7.507616 TCTTCTAGGGTCTCATATTTCTCTTCC 59.492 40.741 0.00 0.00 0.00 3.46
219 243 0.549950 ATTCGTCCTCTCGGGTCCTA 59.450 55.000 0.00 0.00 36.25 2.94
291 315 6.158023 TCGTCTTCTAGGGTTTCATATTCC 57.842 41.667 0.00 0.00 0.00 3.01
332 356 3.144068 TCTCTGGGTTCCCATATTCCA 57.856 47.619 11.26 0.00 35.33 3.53
333 357 3.744530 CGTTCTCTGGGTTCCCATATTCC 60.745 52.174 11.26 0.00 35.33 3.01
359 383 7.690952 TCTGAGTCTTTCTCTAAAGTCCTAC 57.309 40.000 0.00 0.00 42.36 3.18
437 461 5.545723 TCTTCTGAATCTTCCTCTGGAGTTT 59.454 40.000 0.00 0.00 31.21 2.66
443 467 4.710423 TCGTCTTCTGAATCTTCCTCTG 57.290 45.455 0.00 0.00 0.00 3.35
453 477 4.380531 GGATGCCATATTCGTCTTCTGAA 58.619 43.478 0.00 0.00 0.00 3.02
478 502 1.234615 TTTTCCTCTGCGCTTTCCCG 61.235 55.000 9.73 0.00 0.00 5.14
631 656 7.835634 ATGAAAAAGAACCGATCTACTTCTC 57.164 36.000 0.00 0.00 37.42 2.87
686 712 5.102953 TGTCAAGTATCTTTGGGGATGAG 57.897 43.478 0.00 0.00 0.00 2.90
833 864 5.125739 ACCTAATATCTTATCCGCCTCTTCG 59.874 44.000 0.00 0.00 0.00 3.79
986 1021 4.681074 TCGTCCATTTCATATGCCACTA 57.319 40.909 0.00 0.00 0.00 2.74
1102 1137 9.677567 GTGATAAATTCTTTGAGTTAACTTGCA 57.322 29.630 10.02 0.89 0.00 4.08
1148 1183 7.011499 TCCCAATTCACTACTAAGCAAGTTA 57.989 36.000 0.00 0.00 39.80 2.24
1193 1228 1.691196 CTCAACAAGGGAAGCACCAA 58.309 50.000 2.58 0.00 41.20 3.67
1217 1252 6.785488 AATCGCGAATAAGATCATTTGCTA 57.215 33.333 15.24 5.83 41.36 3.49
1275 1310 9.754382 GTCCTATCATACCTTTTTCGTGTATAA 57.246 33.333 0.00 0.00 0.00 0.98
1356 1391 5.528690 TGATTCAATCTTCGCCTTGGAATAG 59.471 40.000 0.00 0.00 0.00 1.73
1437 1472 5.450965 GGATGCCGACAAAATCATCAAAGAT 60.451 40.000 0.00 0.00 37.61 2.40
1774 1812 4.801521 TCCCAAGAATCATGATGGACAT 57.198 40.909 9.46 0.00 40.17 3.06
1873 1912 7.923344 TCACATTTACAATGAAAATTTGACCGT 59.077 29.630 3.47 0.00 31.46 4.83
1896 1936 6.969473 GCTGCTCTTATAACAAAGGAATTCAC 59.031 38.462 7.93 0.00 0.00 3.18
1957 1997 7.775093 TGTAAAGGATTTCTCCATAATGACCAG 59.225 37.037 0.00 0.00 44.79 4.00
2020 2060 6.665680 ACCTTGTGTTATGTCACTAGATCTCT 59.334 38.462 0.00 0.00 41.23 3.10
2050 2090 7.877612 ACACTTCAAAGATTTGTTCCACTTTTT 59.122 29.630 5.29 0.00 39.18 1.94
2074 2114 7.614974 TCAGGGATAATGAATCAATTGAACACA 59.385 33.333 13.09 12.71 36.20 3.72
2154 2194 3.036091 CAATCAAGAATCCCCAAGGCAT 58.964 45.455 0.00 0.00 0.00 4.40
2156 2196 1.758862 CCAATCAAGAATCCCCAAGGC 59.241 52.381 0.00 0.00 0.00 4.35
2220 2260 7.619965 TGGGATCAATAAACCTTTTGGATTTC 58.380 34.615 0.00 0.00 44.07 2.17
2318 2358 6.624861 GCGGAAAAACATTAGACATTCCATCA 60.625 38.462 0.00 0.00 36.89 3.07
2349 2389 5.050091 CCGCTCGCAATAGTCTGATTAATTT 60.050 40.000 0.00 0.00 0.00 1.82
2416 2456 6.902974 AGCCCTTGTTATTCCCAATAAGATTT 59.097 34.615 0.00 0.00 34.23 2.17
2452 2492 6.716628 ACTTGCTTCAGATATGAAACTTTGGA 59.283 34.615 4.06 0.00 0.00 3.53


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.